atgc_shirt1About The Bioinformatics Core

The Bioinformatics core provides expertise and infrastructure to carry out acquisition, curation, distribution of complex data sets as well as to develop and perform computations, analyses and simulations addressing a wide variety of biological questions from genomics and systems biology. The services provided by the core is on a recharge basis.

You may subscribe to the Bioinformatics mailing list for up-to-date news or follow us on twitter at @ucd_biorhythm. Other UCDavis "bio"-twitters: @phylogenomics, @iGenomics

You may access open source tools developed by the Bioinformatics Core at https://trac.genomecenter.ucdavis.edu (First timers need to add security exceptions to their browsers.  University of California software license policy applies to all content on this site )

networkWhat we do

We provide expertise in the following areas:

  • Website Design and Hosting
  • Scientific Database Programming
  • Complex Data Analysis
  • Consulting and Training
  • Computing Resources
  • Software and Database

Resources

The Genome Center Bioinformatics computing clusters consist of an ever evolving group of clusters managed by the UC Davis Genome Center. The clusters are utilized as a collective resource for serial and parallel applications that would be too computationally demanding for smaller research groups to implement. Where one researcher could purchase a small cluster in a grant and hire a system administrator to set it up, it is much more efficient to add computing power to existing infrastructure. This is where the Bioinformatics clusters come into play. For more information, check out the Resources tab.

A few examples of large scale problems the clusters are regularly used for include:

  • Large Scale Sequence Alignment
  • Hidden Markov Model Development and Searches
  • 3D Molecular modeling
  • Mass Spec models
  • Phylogenetic inference

Recent projects

Tetrahymena thermophila micronucleus (MIC) sequence assembly: Dr. Kathleen Collins is coordinating with us in the assembly of internally eliminated sequences (IES) that are spliced out of the chromosomal DNA when the macronucleus (MAC) is generated.  We are using maq-based filtering and the velvet assembler to explore this project.

Comai lab advanced TILLING LIMS system: Dr. Luca Comai and his lab technicians work on deconvolving a series of gene sequences in order to find mutations within the genome. Once mutation candidates are found, Dr. Comai's lab can process chosen candidates and provide more information. This advanced technique provides full mutation pursual in a professional and cost-effective manner. The Bioinformatics Core helps the lab track and work with the orders, as well as provide a clean front-facing user interface complete with order reporting, status updates, and discussions.

Drug Rediscovery Project: The Bioinformatics Core tends a large, multi-source, confidence-rated database of diseases, targets, related pathways, compounds and enzymes, reactions, and more with the ability to track and network the connections between them. Add to that the ability to track the latest research groups studying these factors, and you have a powerful cross-browsing tool for discovery of connections.



If you have any questions, or would like to request more information, feel free to contact us.

Bi-weekly Bioinformatics Tech Forums – Tuesdays 11:00am-12:00pm, Room 4202

The purpose of the Tuesday Bioinformatics Technology Forum (BTF) meeting series at the Genome Center is to provide a campus-wide venue to show and tell how bioinformatics tools or related information technology actually work. To present your practical problems and ask bioinformatics help is also an appropriate thing to do. In the meeting, people are encouraged to do live demonstrations as well as brief introductions of their work or problems. All talks are informal (although introduction slides are often helpful) and active interactions are expected. BTF is operating by a committee, which consists of Kyoungmi Kim and Dawei Lin If you want to talk at BTF, please send an email to lhslin@ucdavis.edu to schedule your talk. BTF meetings are usually held at 11:00am-12:00pm every other Tuesday in room 4202, GBSF.